NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P41181 UniProt NPD GO	AQP2_HUMAN	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.10	-	end	6 *	Cell membrane; apical cell membrane; multi-pass membrane protein. Cytoplasmic vesicle; cytoplasmic v ...	apical plasma membrane [ISS] plasma membrane [TAS]	125800		271
P56402 UniProt NPD GO	AQP2_MOUSE	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.10	-	end	6 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Cytoplasmic vesicl ...	apical plasma membrane [IDA] integral to plasma membrane [TAS] membrane fraction [IDA]			271
P34080 UniProt NPD GO	AQP2_RAT	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.10	-	end	6 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Cytoplasmic vesicl ...	apical plasma membrane [IDA]			271
P37818 UniProt NPD GO	ARGI1_SCHPO	Arginase (EC 3.5.3.1)	0.10	-	cyt	0					323
Q2KJ64 UniProt NPD GO	ARGI1_BOVIN	Arginase-1 (EC 3.5.3.1) (Type I arginase) (Liver-type arginase)	0.10	-	cyt	0	Cytoplasm (By similarity)				322
Q61176 UniProt NPD GO	ARGI1_MOUSE	Arginase-1 (EC 3.5.3.1) (Type I arginase) (Liver-type arginase)	0.10	-	cyt	0	Cytoplasm				323
Q95KM0 UniProt NPD GO	ARGI1_RABIT	Arginase-1 (EC 3.5.3.1) (Type I arginase) (Liver-type arginase)	0.10	-	cyt	0	Cytoplasm				322
Q2TZM9 UniProt NPD GO	RMT2_ASPOR	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.10	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				413
Q5RDG2 UniProt NPD GO	ARMX5_PONPY	Armadillo repeat-containing X-linked protein 5	0.10	-	nuc	0					558
P31752 UniProt NPD GO	ASNS_ASPOF	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (AS)	0.10	-	mit	0					589
P00503 UniProt NPD GO	AATC_PIG	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transa ...	0.10	-	cyt	0	Cytoplasm			1AJS	412
P46643 UniProt NPD GO	AAT1_ARATH	Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix				430
Q95PP1 UniProt NPD GO	API_OSTOS	Aspartyl protease inhibitor precursor	0.10	-	exc	0	Secreted protein (Potential)				227
Q9V751 UniProt NPD GO	ATTB_DROME	Attacin-B precursor	0.10	-	vac	0	Secreted protein	extracellular region [TAS]			218
O96910 UniProt NPD GO	ATT_APLCA	Attractin precursor	0.10	-	exc	0	Secreted protein			1T50	76
Q9H0Y0 UniProt NPD GO	ATG10_HUMAN	Autophagy-related protein 10 (APG10-like)	0.10	-	cyt	0	Cytoplasm (Probable)				220
Q09812 UniProt NPD GO	ATG22_SCHPO	Autophagy-related protein 22	0.10	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				529
Q51LD2 UniProt NPD GO	ATG3_MAGGR	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.10	-	mit	0	Cytoplasm (By similarity)				350
P33488 UniProt NPD GO	ABP4_MAIZE	Auxin-binding protein 4 precursor (ABP)	0.10	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen				204
P49679 UniProt NPD GO	IAA4_PEA	Auxin-induced protein IAA4	0.10	-	cyt	0	Nucleus				189
Q38831 UniProt NPD GO	IAA13_ARATH	Auxin-responsive protein IAA13 (Indoleacetic acid-induced protein 13)	0.10	-	mit	0	Nucleus (By similarity)				247
Q38825 UniProt NPD GO	IAA7_ARATH	Auxin-responsive protein IAA7 (Indoleacetic acid-induced protein 7) (Auxin resistant 2)	0.10	-	nuc	0	Nucleus (By similarity)				243
Q9N1E3 UniProt NPD GO	CD22_PONPY	B-cell receptor CD22 precursor (Siglec-2) (Fragment)	0.10	-	cyt	0	Membrane; single-pass type I membrane protein				330
P30411 UniProt NPD GO	BKRB2_HUMAN	B2 bradykinin receptor (BK-2 receptor) (B2R)	0.10	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	113503		391
Q28642 UniProt NPD GO	BKRB2_RABIT	B2 bradykinin receptor (BK-2 receptor) (B2R)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				367
O35623 UniProt NPD GO	BET1_MOUSE	BET1 homolog (Golgi vesicular membrane-trafficking protein p18) (mBET1)	0.10	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi membrane [IDA]			118
Q12259 UniProt NPD GO	YL108_YEAST	BTB/POZ domain-containing protein YLR108C	0.10	-	cyt	0	Nucleus	nucleus [IDA]			485
P17213 UniProt NPD GO	BPI_HUMAN	Bactericidal permeability-increasing protein precursor (BPI) (CAP 57)	0.10	-	exc	1 *	Membrane-associated in polymorphonuclear Leukocytes (PMN) granules	integral to plasma membrane [TAS]	109195	1EWF	483
Q9BXC9 UniProt NPD GO	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein	0.10	-	nuc	0			606151		721
Q9CWF6 UniProt NPD GO	BBS2_MOUSE	Bardet-Biedl syndrome 2 protein homolog	0.10	-	nuc	0					721
Q864U6 UniProt NPD GO	B3GT3_PIG	Beta-1,3-galactosyltransferase 3 (EC 2.4.1.79) (Beta-1,3-GalTase 3) (Beta3Gal-T3) (b3Gal-T3) (Galact ...	0.10	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				331
Q28044 UniProt NPD GO	ADRB2_BOVIN	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				418
P54833 UniProt NPD GO	ADRB2_CANFA	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				415
P01887 UniProt NPD GO	B2MG_MOUSE	Beta-2-microglobulin precursor	0.10	-	exc	1 *	Secreted protein	integral to plasma membrane [TAS]		2VAB	119
P46626 UniProt NPD GO	ADRB3_BOVIN	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				405
Q9TST4 UniProt NPD GO	ADRB3_FELCA	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				398
P17870 UniProt NPD GO	ARRB1_BOVIN	Beta-arrestin-1 (Arrestin, beta 1)	0.10	-	cyt	0		cytoplasm [ISS] membrane fraction [ISS]		1ZSH	418
Q95223 UniProt NPD GO	ARRB1_RABIT	Beta-arrestin-1 (Arrestin, beta 1)	0.10	-	cyt	0					410
Q7JGM2 UniProt NPD GO	BD01_HYLCO	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.10	-	exc	0	Secreted protein				68
Q7JGM1 UniProt NPD GO	BD01_HYLLA	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.10	-	exc	0	Secreted protein				68
Q95J22 UniProt NPD GO	BD01_HYLML	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.10	-	exc	0	Secreted protein				68
Q5IAB6 UniProt NPD GO	D105A_PANTR	Beta-defensin 105A precursor (Defensin, beta 105A) (Defensin, beta 105) (Beta-defensin 5) (DEFB-5) ( ...	0.10	-	exc	1 *	Secreted protein (By similarity)				78
Q5J5D0 UniProt NPD GO	DB123_MACMU	Beta-defensin 123 precursor (Defensin, beta 123)	0.10	-	mit	0	Secreted protein (Potential)				67
Q30KK5 UniProt NPD GO	DB123_PANTR	Beta-defensin 123 precursor (Defensin, beta 123)	0.10	-	mit	0	Secreted protein (Potential)				67
Q8N688 UniProt NPD GO	DB123_HUMAN	Beta-defensin 123 precursor (Defensin, beta 123) (Beta-defensin 23) (DEFB-23)	0.10	-	mit	0	Secreted protein (Potential)				67
Q30KK1 UniProt NPD GO	DB127_PANTR	Beta-defensin 127 precursor (Defensin, beta 127)	0.10	-	nuc	0	Secreted protein (Potential)				99
P49174 UniProt NPD GO	INVA_MAIZE	Beta-fructofuranosidase, cell wall isozyme precursor (EC 3.2.1.26) (Sucrose hydrolase) (Invertase)	0.10	-	exc	1 *	Cell wall				590
P29416 UniProt NPD GO	HEXA_MOUSE	Beta-hexosaminidase alpha chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acet ...	0.10	-	vac	1 *	Lysosome	lysosome [IDA] membrane [IDA]			528
P07380 UniProt NPD GO	LACB2_HORSE	Beta-lactoglobulin-2 precursor (Beta-LG-2) (Beta-lactoglobulin II) (BLGII) (Minor monomeric beta-lac ...	0.10	-	exc	0	Secreted protein				181
Q29444 UniProt NPD GO	MANBA_BOVIN	Beta-mannosidase precursor (EC 3.2.1.25) (Lysosomal beta A mannosidase) (Mannanase) (Mannase)	0.10	-	mit	0	Lysosome				879

You are viewing entries 64001 to 64050 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.